The Anaconda Project is a direct sequel to the 2003 novelette "The Wallenstein Gambit" which began the neohistorical story expansion toward and into the Eastern half of Europe, the so called "Eastern European thread," and the novel begins soon after the (late 1633) close of The Wallenstein Gambit.

The beginning deals directly with Morris Roth, the Jewish jeweler-protagonist of TWG, who is made General by king Albrecht von Wallenstein, the new king of Bohemia — he'd asked Mike Stearns to consider doing what he could to avert the infamous massacres of Jews in Eastern Europe at least three times, and Stearns cut a deal with Wallenstein who, as the novelette began, claimed that he could avert the pogroms. The book title refers to a military operations map with phase lines, color coded for dating, which snakes eastwards from Bohemia — resembling nothing else so much as a giant anaconda to Roth.

The neohistorical timeline's divergences from our up-time written history become stark as this plot thread opens act II: Wallenstein, a peasant who became famous as a ruthless but extremely capable mercenary general, becomes king of Bohemia, which he wrested (part of The Wallenstein Gambit prequel) from Ferdinand III in the Old Time Line, who was also king of Hungary; and the heir apparent of the pious Ferdinand II, the Habsburg Holy Roman Emperor who was the leading force behind the devastating Thirty Years' War.

But the divergences grow extremely obvious by the end of most of the novels set in 1634 (Four, all more or less running concurrently with one another and with this novel) and in particular at the end of 1634: The Bavarian Crisis. In the neohistorical timeline, Ferdinand III never succeeded his father as "King of the Romans", the predecessor and prerequisite office to being crowned Holy Roman Emperor — whereas in our timeline Ferdinand II lived into 1637, and Ferdinand III succeeded him as Holy Roman Emperor, so the repressive anti-Protestant Habsburg policy remained in place. Another divergence is that, as his dying act, Ferdinand II revoked the Edict of Restitution, a major "secular" reason (greed) underlying the Thirty Years War, creating another departure point for the alternative speculative history.